Magnesium in PDB 3w6p: Crystal Structure of Human DLP1 in Complex with Gdp.ALF4

All present enzymatic activity of Crystal Structure of Human DLP1 in Complex with Gdp.ALF4:
3.6.5.5;

The structure of Crystal Structure of Human DLP1 in Complex with Gdp.ALF4, PDB code: 3w6p was solved by H.Kishida, S.Sugio, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.410, 109.130, 128.730, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 21.4

The structure of Crystal Structure of Human DLP1 in Complex with Gdp.ALF4 also contains other interesting chemical elements:

Fluorine	(F)	8 atoms
Aluminium	(Al)	2 atoms
Calcium	(Ca)	1 atom
Sodium	(Na)	2 atoms

The binding sites of Magnesium atom in the Crystal Structure of Human DLP1 in Complex with Gdp.ALF4 (pdb code 3w6p). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Human DLP1 in Complex with Gdp.ALF4, PDB code: 3w6p:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Human DLP1 in Complex with Gdp.ALF4


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Human DLP1 in Complex with Gdp.ALF4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg803 b:3.1 occ:1.00 O2B A:GDP801 2.0 6.7 1.0 F4 A:ALF802 2.0 11.9 1.0 OG A:SER39 2.1 4.3 1.0 OG1 A:THR59 2.1 6.3 1.0 O A:HOH1102 2.2 5.5 1.0 O A:HOH1101 2.3 8.2 1.0 CB A:THR59 3.1 6.9 1.0 CB A:SER39 3.2 5.1 1.0 PB A:GDP801 3.2 6.3 1.0 F1 A:ALF802 3.4 14.7 1.0 O3B A:GDP801 3.4 5.0 1.0 AL A:ALF802 3.4 8.2 1.0 N A:SER39 3.8 4.9 1.0 CA A:SER39 4.1 4.9 1.0 OD2 A:ASP146 4.1 7.2 1.0 N A:THR59 4.1 7.0 1.0 CG2 A:THR59 4.1 8.1 1.0 CA A:THR59 4.2 7.3 1.0 OD1 A:ASP146 4.2 8.4 1.0 O1B A:GDP801 4.2 4.9 1.0 O A:HOH942 4.3 7.5 1.0 O1A A:GDP801 4.3 7.3 1.0 F2 A:ALF802 4.3 9.4 1.0 O3A A:GDP801 4.4 5.8 1.0 O A:HOH1103 4.5 6.8 1.0 O A:LEU147 4.5 6.6 1.0 CG A:ASP146 4.5 8.1 1.0 O A:PRO52 4.6 9.6 1.0 PA A:GDP801 4.7 6.5 1.0 CB A:LYS38 4.8 4.8 1.0 O2A A:GDP801 4.8 7.0 1.0 C A:LYS38 4.9 5.3 1.0 CE A:LYS38 4.9 7.2 1.0 NZ A:LYS38 5.0 7.0 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Human DLP1 in Complex with Gdp.ALF4


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Human DLP1 in Complex with Gdp.ALF4 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg803 b:3.0 occ:1.00 O2B B:GDP801 2.0 6.6 1.0 F4 B:ALF802 2.0 13.1 1.0 OG B:SER39 2.1 5.9 1.0 OG1 B:THR59 2.1 6.4 1.0 O B:HOH1136 2.2 7.3 1.0 O B:HOH1134 2.3 7.9 1.0 CB B:THR59 3.1 6.8 1.0 CB B:SER39 3.2 5.2 1.0 PB B:GDP801 3.2 5.8 1.0 O3B B:GDP801 3.4 6.1 1.0 F1 B:ALF802 3.4 16.6 1.0 AL B:ALF802 3.5 9.3 1.0 N B:SER39 3.8 4.5 1.0 OD2 B:ASP146 4.0 7.2 1.0 CG2 B:THR59 4.0 6.1 1.0 CA B:SER39 4.1 5.1 1.0 N B:THR59 4.1 7.3 1.0 OD1 B:ASP146 4.1 7.9 1.0 CA B:THR59 4.2 6.6 1.0 O B:HOH961 4.2 7.7 1.0 O1A B:GDP801 4.2 7.0 1.0 O1B B:GDP801 4.3 5.0 1.0 F2 B:ALF802 4.3 10.6 1.0 O3A B:GDP801 4.4 5.0 1.0 O B:HOH1135 4.5 5.0 1.0 CG B:ASP146 4.5 7.6 1.0 O B:LEU147 4.5 7.1 1.0 O B:PRO52 4.6 9.7 1.0 PA B:GDP801 4.7 6.1 1.0 CB B:LYS38 4.8 5.1 1.0 O2A B:GDP801 4.8 7.1 1.0 C B:LYS38 4.9 5.0 1.0 CE B:LYS38 4.9 7.2 1.0

H.Kishida, S.Sugio. Crystal Structure of Gtpase Domain Fused with Minimal Stalks From Human Dynamin-1-Like Protein (DLP1) in Complex with Several Nucleotide Analogues Curr Top Pept Protein Res. V. 14 67 2013.
ISSN: ISSN 0972-4524